Site structure
The site structure that we are going to build is self-contained within a server-root directory. It doesn't matter where this server-root directory is situated on your system; as long as the files within it are located as described here then everything should work OK.
The site structure is as follows (using "/usr/local/ensembl" as an example server-root):
| `-- /usr/local/ensembl | ||||
| |-- apache2 | Apache web server (default installation location) | |||
| |-- bioperl-live | bio-modelling tools that Ensembl is based upon | |||
| |-- ensembl | Ensembl core module | |||
| |-- ensembl-compara | Code for handling cross-species comparisons | |||
| |-- ensembl-funcgen | Code to access the functional genomics data | |||
| |-- ensembl-io | File parsing and writing utilities | |||
| |-- ensembl-orm | Interface to non-genomic databases | |||
| |-- ensembl-tools | API scripts used by online tools such as the VEP | |||
| |-- ensembl-variation | Code to access the variation (SNP) data | |||
| |-- ensembl-webcode | Code to create an Ensembl website | |||
| \-- public-plugins | Public plugin modules | |||